HEADER CELL CYCLE 13-MAY-03 1OGW TITLE SYNTHETIC UBIQUITIN WITH FLUORO-LEU AT 50 AND 67 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-76; COMPND 5 OTHER_DETAILS: LEF IS (4S)-5-FLUORO-L-LEUCINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CHROMOSOMAL PROTEIN, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR D.ALEXEEV,R.RAMAGE,D.W.YOUNG,L.SAWYER REVDAT 6 13-NOV-24 1OGW 1 REMARK REVDAT 5 13-DEC-23 1OGW 1 LINK REVDAT 4 07-DEC-11 1OGW 1 HEADER COMPND KEYWDS REMARK REVDAT 4 2 1 DBREF VERSN REVDAT 3 24-FEB-09 1OGW 1 VERSN REVDAT 2 06-NOV-07 1OGW 1 JRNL REVDAT 1 30-MAY-03 1OGW 0 JRNL AUTH D.ALEXEEV,P.N.BARLOW,S.M.BURY,J.-D.CHARRIER,A.COOPER, JRNL AUTH 2 D.HADFIELD,C.JAMIESON,S.M.KELLY,R.LAYFIELD,R.J.MAYER, JRNL AUTH 3 H.MCSPARRAN,N.C.PRICE,R.RAMAGE,L.SAWYER,B.A.STARKMANN, JRNL AUTH 4 D.UHRIN,J.WILLKEN,D.W.YOUNG JRNL TITL SYNTHESIS, STRUCTURAL AND BIOLOGICAL STUDIES OF UBIQUITIN JRNL TITL 2 MUTANTS CONTAINING (2S, 4S)-5-FLUOROLEUCINE RESIDUES JRNL TITL 3 STRATEGICALLY PLACED IN THE HYDROPHOBIC CORE JRNL REF CHEMBIOCHEM V. 4 894 2003 JRNL REFN ISSN 1439-4227 JRNL PMID 12964166 JRNL DOI 10.1002/CBIC.200300699 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.ALEXEEV,S.M.BURY,M.A.TURNER,O.M.OGUNJOBI,T.W.MUIR, REMARK 1 AUTH 2 R.RAMAGE,L.SAWYER REMARK 1 TITL SYNTHETIC, STRUCTURAL AND BIOLOGICAL STUDIES OF THE REMARK 1 TITL 2 UBIQUITIN SYSTEM REMARK 1 REF BIOCHEM.J. V. 299 159 1994 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 8166634 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.G.LOVE,T.W.MUIR,R.RAMAGE,K.T.SHAW,D.ALEXEEV,L.SAWYER, REMARK 1 AUTH 2 S.M.KELLY,N.C.PRICE,J.E.ARNOLD,M.P.LEE,R.J.MAYER REMARK 1 TITL SYNTHETIC, STRUCTURAL AND BIOLOGICAL STUDIES OF THE REMARK 1 TITL 2 UBIQUITIN SYSTEM: THE SYNTHESIS AND CRYSTAL STRUCTU OF AN REMARK 1 TITL 3 ANALOGUE CONTAINING UNNATURAL AMINO ACIDS REMARK 1 REF BIOCHEM.J. V. 323 727 1997 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 9169606 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.VIJAY-KUMAR,C.E.BUGG,W.J.COOK REMARK 1 TITL STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 194 531 1987 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 3041007 REMARK 1 DOI 10.1016/0022-2836(87)90679-6 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.222 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.222 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 14305 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.214 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 12469 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 114 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 2736.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 3212.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2814 REMARK 3 NUMBER OF RESTRAINTS : 2521 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 ANGLE DISTANCES (A) : 0.100 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.400 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.100 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1290012724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-99 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13828 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXL-97 REMARK 200 STARTING MODEL: PDB ENTRY 1UBI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SEEDED FROM DROP CONTAINING CONTAINING REMARK 280 5 MUL 20MG/ML UBIQUITIN AND 5 MUL 30% PEG 4000 IN 50MM REMARK 280 CACODYLATE-HCL PH 5.6. STORED IN 38% PEG 4000. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 25.42000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.42000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.38500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 LEU (50) AND LEU (67) ARE MODIFIED RESIDUES REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE ARG A 54 O HOH A 2088 1.86 REMARK 500 O HOH A 2071 O HOH A 2072 1.86 REMARK 500 OE1 GLU A 34 O HOH A 2060 2.05 REMARK 500 OE2 GLU A 51 O HOH A 2078 2.13 REMARK 500 O HOH A 2028 O HOH A 2079 2.16 REMARK 500 O HOH A 2055 O HOH A 2057 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2055 O HOH A 2072 4566 1.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 73 -63.31 60.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAR RELATED DB: PDB REMARK 900 DI-UBIQUITIN REMARK 900 RELATED ID: 1C3T RELATED DB: PDB REMARK 900 ROTAMER STRAIN AS A DETERMINANT OF PROTEIN STRUCTURALSPECIFICITY REMARK 900 RELATED ID: 1CMX RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C- TERMINAL REMARK 900 HYDROLASES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 1F9J RELATED DB: PDB REMARK 900 STRUCTURE OF A NEW CRYSTAL FORM OF TETRAUBIQUITIN REMARK 900 RELATED ID: 1FXT RELATED DB: PDB REMARK 900 STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTERCOMPLEX REMARK 900 RELATED ID: 1G6J RELATED DB: PDB REMARK 900 STRUCTURE OF RECOMBINANT HUMAN UBIQUITIN IN AOT REVERSEMICELLES REMARK 900 RELATED ID: 1GJZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF A DIMERIC N-TERMINAL FRAGMENT OF HUMAN REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1NBF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A UBP-FAMILY DEUBIQUITINATING ENZYMEIN REMARK 900 ISOLATION AND IN COMPLEX WITH UBIQUITIN ALDEHYDE REMARK 900 RELATED ID: 1TBE RELATED DB: PDB REMARK 900 TETRAUBIQUITIN REMARK 900 RELATED ID: 1UBI RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1UBQ RELATED DB: PDB REMARK 900 UBIQUITIN DBREF 1OGW A 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEF GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEF HIS LEU VAL LEU ARG LEU ARG GLY GLY MODRES 1OGW LEF A 50 LEU (4S)-5-FLUORO-L-LEUCINE MODRES 1OGW LEF A 67 LEU (4S)-5-FLUORO-L-LEUCINE HET LEF A 50 13 HET LEF A 67 9 HETNAM LEF (4S)-5-FLUORO-L-LEUCINE FORMUL 1 LEF 2(C6 H12 F N O2) FORMUL 2 HOH *114(H2 O) HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 SHEET 1 AA 2 GLN A 2 LYS A 6 0 SHEET 2 AA 2 THR A 12 GLU A 16 -1 O ILE A 13 N VAL A 5 SHEET 1 AB 2 GLN A 41 LEU A 43 0 SHEET 2 AB 2 LEU A 69 LEU A 71 -1 O VAL A 70 N ARG A 42 LINK C GLN A 49 N LEF A 50 1555 1555 1.32 LINK C LEF A 50 N GLU A 51 1555 1555 1.32 LINK C THR A 66 N LEF A 67 1555 1555 1.33 LINK C LEF A 67 N HIS A 68 1555 1555 1.33 CRYST1 50.840 42.770 28.950 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019669 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034542 0.00000